Abstract
Background
Genetic testing for Li-Fraumeni syndrome (LFS) is performed by using blood specimens from patients selected based on phenotype-dependent guidelines. This approach is problematic for understanding the LFS clinical spectrum because patients with nonclassical presentations are missed, clonal hematopoiesis–related somatic blood alterations cannot be distinguished from germline variants, and unrelated tumors cannot be differentiated from those driven by germline TP53 defects.
Methods
To provide insights into the LFS-related cancer spectrum, we analyzed paired tumor-blood DNA sequencing results in 17 922 patients with cancer and distinguished clonal hematopoiesis–related, mosaic, and germline TP53 variants. Loss of heterozygosity and TP53 mutational status were assessed in tumors, followed by immunohistochemistry for p53 expression on a subset to identify those lacking biallelic TP53 inactivation.
Results
Pathogenic/likely pathogenic TP53 variants were identified in 50 patients, 12 (24.0%) of which were clonal hematopoiesis related and 4 (8.0%) of which were mosaic. Twelve (35.3%) of 34 patients with germline TP53 variants did not meet LFS testing criteria. Loss of heterozygosity of germline TP53 variant was observed in 96.0% (95% confidence interval [CI] = 79.7% to 99.9%) of core LFS spectrum–type tumors vs 45.5% (95% CI = 16.8% to 76.6%) of other tumors and 91.3% (95% CI = 72.0% to 98.9%) of tumors from patients who met LFS testing criteria vs 61.5% (95% CI = 31.6% to 86.1%) of tumors from patients who did not. Tumors retaining the wild-type TP53 allele exhibited wild-type p53 expression.
Conclusions
Our results indicate that some TP53 variants identified in blood-only sequencing are not germline and a substantial proportion of patients with LFS are missed based on current testing guidelines. Additionally, a subset of tumors from patients with LFS do not have biallelic TP53 inactivation and may represent cancers unrelated to their germline TP53 defect.
Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder that results from germline pathogenic TP53 variants (1,2) and is associated with a high risk of early-onset malignancies, particularly sarcomas, central nervous system (CNS) tumors, breast cancer, and adrenocortical carcinomas (1,3,4). Several sets of criteria have been developed to identify individuals at risk for LFS and refer them for TP53 genetic testing (5-8). Recently, TP53 testing in broader cancer populations identified pathogenic variants in individuals who do not meet established criteria (9‐11), raising the possibility that the LFS phenotypic spectrum may be wider than previously accepted. A major limitation of these studies and traditional genetic testing approaches is that germline TP53 status is inferred from blood-derived DNA sequencing, while a substantial proportion of apparently heterozygous TP53 variants in blood may be somatic alterations associated with clonal hematopoiesis (CH) (12,13) because TP53 alterations are among the most common CH-related variants (14,15). Additionally, given the high prevalence of cancer, patients with LFS may also develop tumors unrelated to their germline TP53 variant. Hence, differentiating such tumors from TP53-driven cancers is germane to understanding the true phenotypic spectrum of LFS. To provide insights into the TP53-related cancer spectrum in LFS, we used matched tumor-blood analysis in patients with a broad range of solid tumors unselected for hereditary cancer risk.
Methods
Patients
Tumor and blood DNA sequencing using the US Food and Drug Administration–authorized Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) test was offered to patients with advanced cancers treated at Memorial Sloan Kettering Cancer Center. Patients were prospectively offered germline analysis after consenting to tumor sequencing based on an institutional review board–approved protocol. The cohort consisted of 17 922 consecutive patients with a range of solid tumors undergoing MSK-IMPACT testing between July 2015 and April 2020 (16‐18). Compared with the incidence rates reported by the National Cancer Institute Surveillance, Epidemiology, and End Results program (19), our cohort was particularly enriched for pancreatic, ovarian, endometrial/cervical, and CNS cancers as well as sarcomas, while having a relatively lower proportion of lung, head/neck, thyroid, and breast cancers and melanomas (Supplementary Figure 1, available online). Because somatic alterations in the blood are expected to confound germline analysis in individuals with hematologic malignancies, their germline testing is not performed using blood specimens at our institution. Therefore, patients with known circulating hematologic malignancies did not receive this test.
LFS testing criteria (LFS-tc) were determined based on National Comprehensive Cancer Network guidelines (Supplementary Table 1, available online) (7).
Sequencing and Analysis
DNA isolated from tumors and blood was subjected to next-generation sequencing (16). Germline analysis was performed on blood-derived DNA for 76 or 88 genes associated with hereditary cancer predisposition (Supplementary Table 2, available online). Variants were classified based on American College of Medical Genetics and Genomics criteria (20), and those classified as pathogenic or likely pathogenic (P/LP) were further distinguished as germline, mosaic, or CH-related alterations (15). Briefly, variants with a variant allele fraction (VAF) of 20% or more in the blood while being absent from the matched tumor without evidence of loss of heterozygosity (LOH) were classified as CH-related somatic alterations. Variants with a 20%-35% VAF in the blood and a 20% or higher VAF in the tumor were considered mosaic, and all were confirmed by testing another sample type (skin fibroblasts/nail) from the patient. Identification of a heterozygous germline TP53 P/LP variant was considered diagnosis of LFS.
LOH was assessed using the FACETS algorithm (21,22). The allele undergoing LOH was determined based on the VAF of germline TP53 variant in the tumor.
TP53 variant characterizations as loss of function (LOF) and missense with dominant negative, LOF, or unknown impact were obtained from the International Agency for Research on Cancer database (https://p53.iarc.fr).
Statistical Analysis
Differences in LOH rates across different categories were assessed, and P values were calculated using 2-tailed χ2 analysis. A P value less than .05 was considered statistically significant.
Immunohistochemistry for p53 Expression
Immunohistochemistry for p53 was performed on formalin-fixed, paraffin-embedded tissue sections using the monoclonal antibody clone DO-7 (Ventana Medical Systems, Tucson, AZ). Assessment of p53 immunostaining was performed by a pathologist (MHC) blinded to the TP53 LOH status of the tumor and classified as aberrant with diffuse staining pattern, aberrant with complete absence of staining, or wild-type expression pattern.
Results
Identification of Patients With Germline TP53 P/LP Variants
TP53 P/LP variants were identified in 50 (0.28%) of 17 922 patients with cancer, consistent with other large-scale studies (11,23). Twelve (24.0%) of these variants were determined to be somatic CH-related alterations (Supplementary Table 3, available online). VAFs of these alterations ranged between 21% and 44%, with 4 (8.0% of all identified TP53 P/LP variants) having more than 35% VAF, which overlaps with the typical VAF range (35%-65%) used by clinical laboratories to call germline heterozygous variants. Age of patients with CH-related TP53 alterations ranged between 58 and 83 years, with a median age of 70.5 years, consistent with CH detectable by MSK-IMPACT testing being more prevalent in older individuals (12,13).
Thirty-eight patients (0.2% of all patients tested) had germline TP53 P/LP variants (Table 1), and 4 of the variants (10.5% of patients with germline TP53 variants) were mosaic. The remaining 34 (0.19%; 95% confidence interval [CI] = 0.13% to 0.26%) patients were heterozygous for germline TP53 P/LP variants in a nonmosaic fashion (Figure 1, A, Table 1). Age at diagnosis of the first cancer ranged from 1 to 74 years, with a median of 33 years (Figure 1, B). Twenty-four patients (70.6%) were women, and 10 (29.4%) were men. Two patients had whole TP53 gene deletions, 24 had missense, 6 had nonsense, and 1 had a frameshift variant. One patient with 2 LP TP53 variants in cis position was considered heterozygous for the LP c.[375 + 2T>G; 541 C > T] allele.
Table 1.
Patients with Li-Fraumeni syndrome who had germline TP53 P/LP variants identified in the studya
| Patient | No. of tumors analyzed | Age of 1st cancer Dx, y | Sex | Tumors analyzed (age of Dx, y) | Patient’s history of other cancers (age, y) | Meets LFS-tc? | Germline TP53 status | Zygosity |
|---|---|---|---|---|---|---|---|---|
| P1 | 1 | 19 | Male | Osteosarcoma (19) | None | Yes | c.916C>T p. Arg306* (P) | Heterozygous |
| P2 | 1 | 55 | Female | Bladder urothelial carcinoma (55) | None | No | c.374C>T p. Thr125Met (LP) | Heterozygous |
| P3 | 1 | 56 | Male | Leiomyosarcoma (56) | Melanoma (56) | Yes | c.916C>T p. Arg306* (P) | Heterozygous |
| P4 | 1 | 23 | Female | High-grade glioma (25) | Breast cancer (23) | Yes | c.527G>T p. Cys176Phe (LP) | Heterozygous |
| P5 | 1 | 10 | Male | Medulloblastoma (10) | AML (13) | Yes | c.273G>A p. Trp91* (P) | Heterozygous |
| P6 | 2 | 48 | Female | High-grade glioma (55), breast invasive carcinoma (48) | None | No | c.742C>T p. Arg248Trp (P) | Heterozygous |
| P7 | 1 | 5 | Female | Alveolar rhabdomyosarcoma, embryonic subtype (5) | None | Yes | c.713G>C p. Cys238Ser (LP) | Heterozygous |
| P8 | 1 | 33 | Female | Diffuse astrocytoma (33) | Breast cancer (33) | Yes | c.665delC p. Pro222Argfs*25 (P) | Heterozygous |
| P9 | 1 | 16 | Female | Leiomyosarcoma (33) | Melanoma (16), thyroid cancer (27), breast cancer (34) | Yes | c.380C>T p. Ser127Phe (LP) | Heterozygous |
| P10 | 1 | 20 | Female | Ewing sarcoma (39) | Breast cancer (20) | Yes | c.646G>A p. Val216Met (LP) | Heterozygous |
| P11 | 1 | 1 | Male | Choroid plexus carcinoma (1) | None | Yes | c.587G>T p. Arg196Leu (LP) | Heterozygous |
| P12 | 1 | 32 | Female | Duodenal adenocarcinoma (32) | None | No | c.844C>T p. Arg282Trp (P) | Heterozygous |
| P13 | 1 | 12 | Female | Breast invasive carcinoma (29) | Osteosarcoma (12), colorectal cancer (27) | Yes | Whole gene deletion (P) | Heterozygous |
| P14 | 2 | 43 | Male | Pleomorphic liposarcoma (43), pleomorphic rhabdomyosarcoma (43) | Melanoma (44) | Yes | c.524G>A p. Arg175His (P) | Heterozygous |
| P15 | 1 | 51 | Female | Uterine serous carcinoma (62) | Breast cancer (51, 54), basal cell carcinoma (62) | No | c.1024C>T p. Arg342* (P) | Heterozygous |
| P16 | 2 | 28 | Female | Sarcoma (28), undifferentiated pleomorphic sarcoma (28) | None | Yes | c.535C>T p. His179Tyr (P) | Heterozygous |
| P17 | 1 | 51 | Male | Prostate adenocarcinoma (51) | Gastric cancer (55) | No | c.1010G>A p. Arg337His (P) | Heterozygous |
| P18 | 1 | 4 | Male | Leiomyosarcoma (27) | Rhabdomyosarcoma (4) | Yes | c.154C>T p. Gln52* (P) | Heterozygous |
| P19 | 1 | 53 | Female | Colorectal adenocarcinoma (53) | None | No | c.542G>A p. Arg181His (P) | Heterozygous |
| P20 | 2 | 60 | Male | Gastrointestinal stromal tumor (69), leiomyosarcoma (61) | Prostate cancer (60), lung cancer (66) | Yes | c.473G>A p. Arg158His (P) | Heterozygous |
| P21 | 1 | 12 | Female | Renal medullary carcinoma (23) | Osteosarcoma (12) | Yes | c.1025G>C p. Arg342Pro (P) | Heterozygous |
| P22 | 1 | 36 | Female | Radiation-associated sarcoma (45) | Breast cancer (36) | Yes | c.799C>T p. Arg267Trp (P) | Heterozygous |
| P23 | 2 | 18 | Female | Sarcoma (18), undifferentiated pleomorphic sarcoma (18) | None | Yes | c.524G>A p. Arg175His (P) | Heterozygous |
| P24 | 1 | 35 | Female | Leiomyosarcoma (35) | None | Yes | c.718A>G p. Ser240Gly (LP) | Heterozygous |
| P25 | 1 | 1 | Female | Neuroblastoma (1) | None | No | c.818G>A p. Arg273His (P) | Heterozygous |
| P26 | 1 | 44 | Male | Lung adenocarcinoma (44) | None | No | c.844C>T p. Arg282Trp (P) | Heterozygous |
| P27 | 2 | 74 | Female | Lung squamous cell carcinoma (74), colon adenocarcinoma (75) | None | No | c.733G>A p. Gly245Ser (P) | Heterozygous |
| P28 | 1 | 25 | Male | Medulloblastoma (25) | None | No | c.614A>G p. Tyr205Cys (P) | Heterozygous |
| P29 | 1 | 20 | Female | High-grade glioma, NOS (20) | None | Yes | c.794T>A p. Leu265Gln (LP) | Heterozygous |
| P30 | 1 | 37 | Female | Uterine leiomyosarcoma (37) | None | Yes | Whole gene deletion (P) | Heterozygous |
| P31 | 1 | 39 | Female | High-grade serous ovarian cancer (40) | Breast cancer (39) | No | c.309C>G p. Tyr103* (P) | Heterozygous |
| P32 | 1 | 29 | Female | Radiation-associated undifferentiated pleomorphic sarcoma (38) | Breast cancer (29) | Yes | c.841G>C p. Asp281His (LP) | Heterozygous |
| P33 | 1 | 51 | Female | Leiomyosarcoma (51) | Breast cancer (46) | Yes | c.799C>G p. Arg267Gly (LP) | Heterozygous |
| P34 | 1 | 43 | Female | Breast invasive ductal carcinoma (43) | None | No | c.[375 + 2T>G; 541 C > T] p.(?) (LP) | Heterozygous |
| P35 | 1 | 27 | Female | Osteosarcoma (27) | None | No | c.216delC p. Val73Trpfs*50 (P) | Mosaic (20% VAF) |
| P36 | 1 | 57 | Male | Adenocarcinoma of the gastroesophageal junction (57) | AML | No | c.844C>G p. Arg282Gly (P) | Mosaic (32% VAF) |
| P37 | 1 | 32 | Female | Breast invasive ductal carcinoma (32) | None | No | c.247_256delGCGGCCCCTG p. Ala83Hisfs*37 (P) | Mosaic (28% VAF) |
| P38 | 1 | 48 | Female | Breast invasive ductal carcinoma (48) | Lung adenocarcinoma (56), AML (57) | No | c.796G>T p. Gly266* (P) | Mosaic (34% VAF) |
AML = acute myeloid leukemia; Dx = diagnosis; LFS-tc = Li-Fraumeni syndrome testing criteria; LP = likely pathogenic; NOS = not otherwise specified; P = pathogenic; VAF = variant allele fraction.
Figure 1.
Cancer characteristics of patients identified with germline TP53 P/LP variants in the study. A) Presenting tumor types of the patients who had matched tumor -normal DNA sequencing in the study. Numbers above the bars represent the number of the patients with germline TP53 P/LP variants. B) Age at diagnosis of first cancer in patients with germline TP53 P/LP variants. C) Spectrum of the 40 tumors from patients with germline TP53 P/LP variants that were analyzed in the study. GIST = gastrointestinal stromal tumor; LFS = Li-Fraumeni syndrome; P/LP = pathogenic or likely pathogenic.
Twelve (35.3%) of 34 patients heterozygous for P/LP TP53 variants did not meet LFS-tc (5‐8). None of the 4 patients with mosaic variants met LFS-tc, and the proportion of patients with germline TP53 P/LP variants who did not meet LFS-tc, including patients with mosaic variants, was 42.1% (16 of 38). None of the patients had P/LP variants in other highly penetrant cancer predisposition genes tested (Supplementary Table 2, available online). One patient carried a pathogenic ATM variant.
Matched Tumor Analysis in Patients With Germline TP53 P/LP Variants
Forty tumor samples from 34 patients heterozygous for germline TP53 P/LP variants were sequenced using the MSK-IMPACT test (Table 1). In patients who met LFS-tc, 23 (88.5%) of 26 tumors were 1 of the core LFS spectrum tumors (defined as osteosarcoma and soft tissue sarcoma [except Ewing sarcoma], brain/CNS tumor, adrenocortical carcinoma, and breast carcinoma) (5,6), whereas 3 (11.5%) were not (Figure 1, C). Tumors outside the core LFS spectrum identified in patients who met LFS-tc were a gastrointestinal stromal tumor, a Ewing sarcoma, and a kidney medullary carcinoma from a patient with sickle cell trait, which is typically associated with development of this cancer (24). In patients who did not meet LFS-tc, 4 (28.6%) of 14 tumors were core LFS spectrum–type tumors, whereas 10 (71.4%) were not.
To assess whether biallelic TP53 inactivation was present in tumors, we analyzed the somatic LOH status of the allele harboring the germline TP53 variant and the presence of another somatic TP53 alteration (second hit). TP53 LOH status could be determined in 36 tumors with sufficient purity (≥25%). LOH of the allele harboring the germline TP53 variant, with either physical or copy number–neutral loss of the wild-type allele, was observed in 29 (80.6%) of 36 tumors, with a rate of 96.0% (24 of 25; 95% CI = 79.7% to 99.9%) in the core LFS spectrum–type tumors vs 45.5% (5 of 11; 95% CI = 16.8% to 76.6%) in other tumors (P = .0004; Figure 2, Table 2). None of the tumors without LOH at the TP53 locus had an oncogenic second TP53 alteration, consistent with observations that losing the wild-type allele is a more common mechanism than another somatic alterations for biallelic TP53 inactivation (25,26). Of note, a bladder urothelial carcinoma had a TP53 p. Glu388Lys somatic alteration located outside the known functional domains of p53 and had not been reported to affect protein function in the literature. Although a possible oncogenic role of this variant cannot be ruled out, it was considered to have uncertain significance based on available data. LOH of the germline TP53 variant (loss of wild-type allele) was observed in 91.3% (21 of 23; 95% CI = 72.0% to 98.9%) of the tumors from patients who met LFS-tc compared with 61.5% (8 of 13; 95% CI = 31.6% to 86.1%) of the tumors from patients who did not meet LFS-tc (P = .03) (Figure 2). All (21 of 21) core LFS spectrum–type tumors from patients who met LFS-tc had LOH of the germline TP53 variant compared with 75.0% (3 of 4) of such tumors from patients who did not meet LFS-tc, although the number of core LFS spectrum–type tumors from patients who did not meet LFS-tc available for analysis was too small to make a conclusive comparison. Two tumors had loss of germline TP53-mutant allele with retention of wild-type allele: an invasive breast carcinoma (estrogen receptor positive, progesterone receptor positive, HER2 negative) diagnosed at 48 years of age and a colorectal adenocarcinoma diagnosed at 53 years of age, both from patients who did not meet LFS-tc.
Figure 2.
LOH at the TP53 locus in tumors from patients with germline TP53 P/LP variants. A) Top panel: Number of tumors with loss of the wild-type allele (LOH of the germline TP53 variant allele) (red), no LOH at the TP53 locus (gray), or loss of the germline TP53 variant allele (green) are presented. Bottom panel: Percentage of LOH at the TP53 locus is compared between tumors from patients who met vs patients who did not meet LFS genetic testing criteria (left) and tumors within or outside the core LFS spectrum types (right). P values were calculated using 2-tailed χ2 analysis. B) LOH at the TP53 locus in tumors belonging to each tumor type. C) LOH at the TP53 locus in tumors based on age at diagnosis. GIST = gastrointestinal stromal tumor; LFS = Li-Fraumeni syndrome; LFStc+ = Li-Fraumeni syndrome testing criteria positive; LOH = loss of heterozygosity; P/LP = pathogenic or likely pathogenic.
Table 2.
Analysis of the presence or absence of TP53 loss of heterozygosity and somatic second-hit TP53 alteration in tumors
| Tumor type | Patient | Age at Dx, y | Meets LFS-tc? | Core LFS tumor type? | LOH/2nd hit in TP53? |
|---|---|---|---|---|---|
| Tumors without LOH of germline TP53 variant | |||||
| Bladder urothelial carcinoma | P2 | 55 | No | No | No |
| Ewing sarcoma | P10 | 39 | Yes | No | No |
| Prostate adenocarcinoma | P17 | 51 | No | No | No |
| Gastrointestinal stromal tumor | P20 | 69 | Yes | No | No |
| Neuroblastoma | P25 | 1 | No | No | No |
| Breast invasive carcinomaa | P6 | 48 | No | Yes | Loss of germline TP53 mutant allele |
| Colorectal adenocarcinoma | P19 | 53 | No | No | Loss of germline TP53 mutant allele |
| Tumors with LOH of the germline TP53 variant | |||||
| Osteosarcoma | P1 | 19 | Yes | Yes | LOH |
| Leiomyosarcoma | P3 | 56 | Yes | Yes | LOH |
| High-grade glioma | P4 | 25 | Yes | Yes | LOH |
| Medulloblastoma | P5 | 10 | Yes | Yes | LOH |
| High-grade gliomaa | P6 | 55 | No | Yes | LOH |
| Alveolar rhabdomyosarcoma, embryonic subtype | P7 | 5 | Yes | Yes | LOH |
| Diffuse astrocytoma | P8 | 33 | Yes | Yes | LOH |
| Leiomyosarcoma | P9 | 33 | Yes | Yes | LOH |
| Choroid plexus carcinoma | P11 | 1 | Yes | Yes | LOH |
| Duodenal adenocarcinoma | P12 | 32 | No | No | LOH |
| Breast invasive carcinoma | P13 | 29 | Yes | Yes | LOH |
| Pleomorphic liposarcomaa | P14 | 43 | Yes | Yes | LOH |
| Pleomorphic rhabdomyosarcomaa | P14 | 43 | Yes | Yes | LOH |
| Sarcomaa | P16 | 28 | Yes | Yes | LOH |
| Undifferentiated pleomorphic sarcomaa | P16 | 28 | Yes | Yes | LOH |
| Leiomyosarcoma | P18 | 27 | Yes | Yes | LOH |
| Radiation-associated sarcoma | P22 | 45 | Yes | Yes | LOH |
| Undifferentiated pleomorphic sarcomaa | P23 | 18 | Yes | Yes | LOH |
| Sarcomaa | P23 | 18 | Yes | Yes | LOH |
| Leiomyosarcoma | P24 | 35 | Yes | Yes | LOH |
| Lung adenocarcinoma | P26 | 44 | No | No | LOH |
| Lung squamous cell carcinomaa | P27 | 74 | No | No | LOH |
| Colon adenocarcinomaa | P27 | 75 | No | No | LOH |
| Medulloblastoma | P28 | 25 | No | Yes | LOH |
| High-grade glioma, NOS | P29 | 20 | Yes | Yes | LOH |
| High-grade serous ovarian cancer | P31 | 40 | No | No | LOH |
| Radiation-associated undifferentiated pleomorphic sarcoma | P32 | 38 | Yes | Yes | LOH |
| Leiomyosarcoma | P33 | 51 | Yes | Yes | LOH |
| Breast invasive ductal carcinoma | P34 | 43 | No | Yes | LOH |
| Tumors for which TP53 LOH status could not be assessed | |||||
| Uterine serous carcinoma | P15 | 62 | No | No | NA |
| Leiomyosarcoma | P20 | 61 | Yes | Yes | NA |
| Kidney medullary carcinoma | P21 | 23 | Yes | No | NA |
| Uterine leiomyosarcoma | P30 | 37 | Yes | Yes | NA |
Tumor from a patient who had multiple tumor samples analyzed in the study. Dx = diagnosis; LFS = Li-Fraumeni syndrome; LFS-tc = Li-Fraumeni syndrome testing criteria; LOH = loss of heterozygosity; NA = not assessed; NOS = not otherwise specified.
Five patients had multiple tumors available for analysis, including the patient described above with a breast carcinoma that had lost the germline TP53-mutant allele. This patient also had a high-grade glioma diagnosed at 56 years of age that had loss of the wild-type TP53 allele, suggesting that both germline TP53 variant-related and unrelated tumors may develop in patients with LFS. All 6 core LFS spectrum–type tumors available from 3 patients who met LFS-tc had LOH of the germline TP53 variant. Finally, both tumors outside the core LFS spectrum (a lung squamous cell carcinoma and a colon adenocarcinoma) from a patient who did not meet LFS-tc had LOH of the germline TP53 variant.
LFS Tumors Without LOH of the Germline TP53 Variant
Seven (20.6%) of 34 patients with LFS had a tumor without LOH at the TP53 locus or with loss of the germline TP53-mutant allele (Table 2): a Ewing sarcoma with EWSR1-FLI1 fusion, a gastrointestinal stromal tumor with oncogenic KIT p. Trp557Arg alteration, a neuroblastoma with MYCN amplification, a colorectal adenocarcinoma, a bladder urothelial carcinoma, a prostate adenocarcinoma, and an invasive breast carcinoma. Five were available for p53 immunohistochemistry, and all uniformly displayed the wild-type p53 expression pattern, consistent with the absence of biallelic TP53 defect (Table 3, Figure 3). Immunohistochemistry was also performed on a glioma sample from the patient who had a breast carcinoma with loss of the germline TP53-mutant allele. The glioma with loss of the wild-type allele exhibited an aberrant diffuse staining pattern (Figure 3) consistent with biallelic TP53 inactivation, whereas the breast carcinoma with loss of the germline TP53-mutant allele from the same patient showed a wild-type p53 expression pattern consistent with retained p53 function.
Table 3.
Results of immunohistochemistry for p53 in tumors
| Tumor type | Patient | LOH/2nd hit for TP53? | IHC for p53 protein |
|---|---|---|---|
| High-grade gliomaa | P6 | LOH | Aberrant diffuse staining pattern |
| Breast invasive carcinomaa | P6 | Loss of germline TP53 mutant allele | Wildtype expression pattern |
| Ewing sarcoma | P10 | No | Wildtype expression pattern |
| Prostate adenocarcinoma | P17 | No | Wildtype expression pattern |
| Gastrointestinal stromal tumor | P20 | No | Wildtype expression pattern |
| Neuroblastoma | P25 | No | Wildtype expression pattern |
Tumor from a patient who had multiple tumor samples analyzed in the study. IHC = immunohistochemistry; LOH = loss of heterozygosity.
Figure 3.
Immunohistochemistry for p53 expression. Two tumors from patient P6 were examined, and the glioma that had LOH of the germline TP53 variant exhibited an aberrant diffuse expression pattern, whereas the breast carcinoma that had loss of the allele harboring the germline TP53 variant showed a wild-type p53 expression pattern. Tumors from patients P10, P17, P20, and P25 that did not have LOH at the TP53 locus exhibited wild-type p53 expression pattern. Scale bars represent 100 µm. LOH = loss of heterozygosity.
Five of the 7 (71.4%) patients who had tumors without LOH at the TP53 locus or with loss of the germline TP53-mutant allele did not meet LFS-tc. One of these patients, who developed prostate cancer at 51 years of age and stomach cancer at 55 years of age, harbored the TP53 p. Arg337His variant known to have lower penetrance compared with typical TP53 pathogenic variants (27‐29). Six were outside the core LFS spectrum, and 1 breast carcinoma was diagnosed when the patient was 48 years of age.
Many TP53 missense variants have been characterized as dominant negative (30‐32). Although results have varied regarding the selective pressure for dominant-negative TP53 variants during tumorigenesis, recent large-scale analyses have demonstrated that such variants undergo LOH at a rate similar to LOF variants (25,26,33), suggesting that cells carrying these variants may also be under selective pressure to lose the wild-type allele. To understand whether the absence of LOH could be explained by the presence of dominant-negative variants, we compared the LOH rate based on TP53 variant types and did not observe a statistically significant difference between the LOH rate in tumors with LOF variants vs dominant-negative variants (Supplementary Figure 2, available online). Two of 7 patients with tumors that retained the wild-type allele had variants characterized as dominant negative (p.Arg248Trp, p. Arg273His), including the p. Arg248Trp variant, which was somatically lost in the breast carcinoma. Thus, although 1 possibility for the absence of LOH of the germline TP53 variant may be lower selective pressure for potential dominant-negative variants to lose the normal allele during tumorigenesis, other possibilities include the development of tumors independent of their germline TP53 defect.
Discussion
Our understanding of the TP53-related cancer spectrum has changed drastically over the years (5,34). There is currently a discordance between the stringent clinical definition of LFS, with its molecular definition of carrying a pathogenic germline TP53 variant, that refers to a range of phenotypes, as demonstrated by our results and other recent studies (10,11,34). In fact, both definitions should refer to the same risk estimates, which have substantial implications for a patient’s management, including treatment of ongoing cancers (ie, avoiding radiation therapy) (5,7,35‐37) and future surveillance (5,34,38,39). Frebourg et al. (34) proposed reconsidering the LFS definition in light of the diverse phenotypes associated with germline TP53 alterations to refer to a wider multicancer predisposition syndrome. Our results support this argument and underscore the need to expand TP53 genetic testing criteria. It is becoming clear that relying on family history to select high-risk individuals is problematic. Regardless of family history, TP53 P/LP variants have been identified in a large proportion of patients with certain cancers (40‐45). Additionally, de novo TP53 variants contribute 7%-20% of disease (46,47). The p. Arg337His variant demonstrates that TP53 variants may have low penetrance (27‐29). For these reasons, extending TP53 testing to patients who lack family history but have suggestive clinical presentations would be imperative. Finally, 10.5% of patients with germline TP53 variants in our study were mosaic, and none of them met LFS-tc. This ratio is higher than the approximately 3% of mosaic individuals identified among patients with germline TP53 variants who met Chompret criteria (47), suggesting that widening the testing criteria may also identify additional mosaic patients. Because mosaic individuals are more likely to have milder presentations and expected to lack family history, they are more likely to be missed by current testing guidelines.
Our results provide an unbiased rate of CH-related TP53 alterations that may be mistaken as germline in blood-only sequencing of patients with cancer because all detected variants were assessed for their status in matched tumors and demonstrate that a substantial proportion of TP53 variants assumed to be germline in blood-only sequencing, especially in older individuals, may in fact represent CH, leading to an incorrect LFS diagnosis. Although CH-related TP53 alterations are more frequent in older individuals (12,13), they have also been described in younger patients (12,48), suggesting that they may also confound genetic testing in younger adults.
Because many cancers are common, tumors unrelated to their TP53 variant may also develop in patients with LFS. We evaluated whether a molecular analysis of LFS tumors may help distinguish those that occur unrelated to their germline TP53 alteration. Although the absence of a somatic second hit cannot establish that the germline variant was not a driver in tumorigenesis, loss of the wild-type allele or a second TP53 alteration is observed in approximately 90% of TP53-mutant cancers (25,33). Our results suggest that tumors outside the core LFS spectrum and those identified in patients who do not meet LFS-tc may be more likely to lack a second somatic TP53 hit. Hughley et al. suggested that the relative risk of germline pathogenic variants in tumor-suppressor genes for a cancer type can be estimated by the observed biallelic inactivation rate of the gene in the particular tumor type (49). In our study, only 4% of core LFS spectrum–type tumors vs 55% of tumors outside the core LFS spectrum lacked a second hit, consistent with observations that biallelic inactivation state may reflect relative risk for a particular tumor (49). Based on this model, in patients with LFS, 1 of 25 tumors within core LFS spectrum may develop independent of the germline TP53 alteration, as expected based on the high risk for these tumors, whereas approximately half of tumors outside the core LFS spectrum may be driven by the germline TP53 variant. Although a dominant-negative impact of variants that may bypass the need to lose the normal allele during tumorigenesis cannot be ruled out, one possibility is that at least a subset of these tumors may presumably be unrelated to the germline TP53 alteration. Further functional experiments on p53 and other driver genes may elucidate the contribution of germline TP53 defects to the development of these tumors.
Detection of TP53 P/LP variants in individuals with diverse presentations creates additional challenges in estimating future cancer risk in carriers. Earlier studies on familial cases likely suffered from ascertainment bias, resulting in overestimation of disease risks (6,37,50). Patient cohorts referred for clinical TP53 genetic testing are also likely enriched for individuals who meet current testing criteria (10,11,23). Large case-control studies (51) and prospective analyses of carriers identified through comprehensive testing will provide more accurate disease risk estimations.
Our study has several limitations. Despite the large cohort, the sample size of patients with LFS identified and the number of available tumors were limited. Additionally, hematologic malignancies were not included. We did not have reliable race/ethnicity data from our patients; therefore, any potential impact of race/ethnicity distribution of the cohort or rare founder variants in certain populations on the results cannot be excluded. Our assay provided high coverage for TP53 coding regions, but the possibility of missing clinically significant alterations in coding or noncoding regions cannot be excluded. Finally, limitations in LOH detection cannot be ruled out (21).
Matched tumor-normal sequencing in a broad cancer population without selection based on hereditary cancer risk revealed LFS in individuals who would be missed using traditional testing. Paired tumor-normal analysis may refine implications of a germline TP53 variant identified in a patient and provide insights into the true phenotypic spectrum of LFS as well as other hereditary cancer syndromes.
Funding
This work was partly supported by the Marie-Josée and Henry R. Kravis Center for Molecular Oncology, the Precision, Interception and Prevention Program; the Robert and Kate Niehaus Center for Inherited Cancer Genomics; and the National Institutes of Health/National Cancer Institute Cancer Center Support Grant (P30 CA008748). JSR-F is funded in part by the Breast Cancer Research Foundation and by the National Institutes of Health/National Cancer Institute grant (P50 CA247749 01).
Notes
Role of the funders: The funding sources had no role in the study design, collection, analysis, and interpretation of the data, or writing of the manuscript.
Disclosures: JSR-F reports receiving personal/consultancy fees from Goldman Sachs, REPARE Therapeutics and Paige.AI, membership of the scientific advisory boards of VolitionRx, REPARE Therapeutics and Paige.AI, membership of the Board of Directors of Grupo Oncoclinicas, and ad hoc membership of the scientific advisory boards of Roche Tissue Diagnostics, Ventana Medical Systems, Novartis, Genentech and InVicro, outside the scope of this study. All remaining authors have declared no conflicts of interest.
Author contributions: Study conception and design: OCB, JRF, DM; Acquisition of data: all authors; Data analysis and interpretation: OCB, PS, MHC, JRF, DM; Writing of manuscript: OCB, JRF, DM; Review and final approval of manuscript: all authors.
Data Availability
Deidentified molecular data from LFS tumors in the study are available upon request.
Supplementary Material
Contributor Information
Ozge Ceyhan-Birsoy, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Pier Selenica, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
M Herman Chui, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Gowtham Jayakumaran, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Ryan Ptashkin, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Maksym Misyura, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Umut Aypar, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Sowmya Jairam, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Ciyu Yang, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Yirong Li, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Nikita Mehta, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Yelena Kemel, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Erin Salo-Mullen, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Anna Maio, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Margaret Sheehan, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Ahmet Zehir, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Maria Carlo, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Alicia Latham, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Zsofia Stadler, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Mark Robson, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Kenneth Offit, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Marc Ladanyi, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Michael Walsh, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Jorge S Reis-Filho, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Diana Mandelker, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
References
- 1. Li FP, Fraumeni JF Jr. Soft-tissue sarcomas, breast cancer, and other neoplasms. A familial syndrome? Ann Intern Med. 1969;71(4):747–752. doi:10.7326/0003-4819-71-4-747. [5360287] [DOI] [PubMed] [Google Scholar]
- 2. Malkin D, Li FP, Strong LC, et al. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science. 1990;250(4985):1233–1238. doi:10.1126/science.1978757. [1978757] [DOI] [PubMed] [Google Scholar]
- 3. Garber JE, Goldstein AM, Kantor AF, Dreyfus MG, Fraumeni JF Jr, Li FP. Follow-up study of twenty-four families with Li-Fraumeni syndrome. Cancer Res. 1991;51(22):6094–6097. [PubMed] [Google Scholar]
- 4. Li FP, Fraumeni JF Jr, Mulvihill JJ, et al. A cancer family syndrome in twenty-four kindreds. Cancer Res. 1988;48(18):5358–5362. [PubMed] [Google Scholar]
- 5. Bougeard G, Renaux-Petel M, Flaman JM, et al. Revisiting Li-Fraumeni syndrome from TP53 mutation carriers. J Clin Oncol. 2015;33(21):2345–2352. doi:10.1200/JCO.2014.59.5728. [DOI] [PubMed] [Google Scholar]
- 6. Chompret A, Abel A, Stoppa-Lyonnet D, et al. Sensitivity and predictive value of criteria for p53 germline mutation screening. J Med Genet. 2001;38(1):43–47. doi:10.1136/jmg.38.1.43. [11332399] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Genetic/Familial High-Risk Assessment: Breast and Ovarian. Version 3. National Comprehensive Cancer Network. www.nccn.org. Published January 18, 2019. Accessed July 21, 2021.
- 8. Tinat J, Bougeard G, Baert-Desurmont S, et al. 2009 version of the Chompret criteria for Li Fraumeni syndrome. J Clin Oncol. 2009;27(26):e108–109; author reply e110. doi:10.1200/JCO.2009.22.7967. [19652052] [DOI] [PubMed] [Google Scholar]
- 9. Kamihara J, Rana HQ, Garber JE. Germline TP53 mutations and the changing landscape of Li-Fraumeni syndrome. Hum Mutat. 2014;35(6):654–662. doi:10.1002/humu.22559. [24706533] [DOI] [PubMed] [Google Scholar]
- 10. Rana HQ, Clifford J, Hoang L, et al. Genotype-phenotype associations among panel-based TP53+ subjects. Genet Med. 2019;21(11):2478–2484. doi:10.1038/s41436-019-0541-y. [31105275] [DOI] [PubMed] [Google Scholar]
- 11. Rana HQ, Gelman R, LaDuca H, et al. Differences in TP53 mutation carrier phenotypes emerge from panel-based testing. J Natl Cancer Inst. 2018;110(8):863–870. doi:10.1093/jnci/djy001. [DOI] [PubMed] [Google Scholar]
- 12. Coffee B, Cox HC, Bernhisel R, et al. A substantial proportion of apparently heterozygous TP53 pathogenic variants detected with a next-generation sequencing hereditary pan-cancer panel are acquired somatically. Hum Mutat. 2020;41(1):203–211. doi:10.1002/humu.23910. [31490007] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Weitzel JN, Chao EC, Nehoray B, et al. Somatic TP53 variants frequently confound germ-line testing results. Genet Med. 2018;20(8):809–816. doi:10.1038/gim.2017.196. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Coombs CC, Zehir A, Devlin SM, et al. Therapy-related clonal hematopoiesis in patients with non-hematologic cancers is common and associated with adverse clinical outcomes. Cell Stem Cell. 2017;21(3):374–382.e4. doi:10.1016/j.stem.2017.07.010. [28803919] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Ptashkin RN, Mandelker DL, Coombs CC, et al. Prevalence of clonal hematopoiesis mutations in tumor-only clinical genomic profiling of solid tumors. JAMA Oncol. 2018;4(11):1589–1593. doi:10.1001/jamaoncol.2018.2297. [29872864] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16. Cheng DT, Mitchell TN, Zehir A, et al. Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. J Mol Diagn. 2015;17(3):251–264. doi:10.1016/j.jmoldx.2014.12.006. [25801821] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Mandelker D, Zhang L, Kemel Y, et al. Mutation detection in patients with advanced cancer by universal sequencing of cancer-related genes in tumor and normal DNA vs guideline-based germline testing. JAMA. 2017;318(9):825–835. doi:10.1001/jama.2017.11137. [28873162] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18. Zehir A, Benayed R, Shah RH, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med. 2017;23(6):703–713. doi:10.1038/nm.4333. [28481359] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19. Howlader NN, Krapcho M, Miller D, et al. , eds. SEER Cancer Statistics Review (CSR) 1975-2017. https://seer.cancer.gov/csr/1975_2017/. Published April 15, 2020. Accessed June 19, 2021.
- 20. Richards S, Aziz N, Bale S, et al. ; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–424. doi:10.1038/gim.2015.30. [25741868] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21. Shen R, Seshan VE. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 2016;44(16):e131. doi:10.1093/nar/gkw520. [27270079] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22. Piscuoglio S, Ng CKY, Murray MP, et al. The genomic landscape of male breast cancers. Clin Cancer Res. 2016;22(16):4045–4056. doi:10.1158/1078-0432.CCR-15-2840. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 23. LaDuca H, Polley EC, Yussuf A, et al. A clinical guide to hereditary cancer panel testing: evaluation of gene-specific cancer associations and sensitivity of genetic testing criteria in a cohort of 165,000 high-risk patients. Genet Med. 2020;22(2):407–415. doi:10.1038/s41436-019-0633-8. [31406321] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24. Ataga KI, Orringer EP. Renal abnormalities in sickle cell disease. Am J Hematol. 2000;63(4):205–211. doi:10.1002/(sici)1096-8652(200004)63:4<205::AID-AJH8>3.0.CO;2-8. [DOI] [PubMed] [Google Scholar]
- 25. Donehower LA, Soussi T, Korkut A, et al. Integrated analysis of TP53 gene and pathway alterations in the cancer genome atlas. Cell Rep. 2019;28(11):3010. doi:10.1016/j.celrep.2019.08.061. [31509758] [DOI] [PubMed] [Google Scholar]
- 26. Stoczynska-Fidelus E, Szybka M, Piaskowski S, et al. Limited importance of the dominant-negative effect of TP53 missense mutations. BMC Cancer. 2011;11:243. doi:10.1186/1471-2407-11-243. [21668955] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 27. Achatz MIW, Olivier M, Le Calvez F, et al. The TP53 mutation, R337H, is associated with Li-Fraumeni and Li-Fraumeni-like syndromes in Brazilian families. Cancer Lett. 2007;245(1-2):96–102. doi:10.1016/j.canlet.2005.12.039. [16494995] [DOI] [PubMed] [Google Scholar]
- 28. Palmero EI, Schüler-Faccini L, Caleffi M, et al. Detection of R337H, a germline TP53 mutation predisposing to multiple cancers, in asymptomatic women participating in a breast cancer screening program in southern Brazil. Cancer Lett. 2008;261(1):21–25. doi:10.1016/j.canlet.2007.10.044. [18248785] [DOI] [PubMed] [Google Scholar]
- 29. Ribeiro RC, Rodriguez-Galindo C, Figueiredo BC, et al. Germline TP53 R337H mutation is not sufficient to establish Li-Fraumeni or Li-Fraumeni-like syndrome. Cancer Lett. 2007;247(2):353–355. author reply 356-8. doi:10.1016/j.canlet.2006.04.008. [DOI] [PubMed] [Google Scholar]
- 30. Dearth LR, Qian H, Wang T, et al. Inactive full-length p53 mutants lacking dominant wild-type p53 inhibition highlight loss of heterozygosity as an important aspect of p53 status in human cancers. Carcinogenesis. 2007;28(2):289–298. doi:10.1093/carcin/bgl132. [16861262] [DOI] [PubMed] [Google Scholar]
- 31. Giacomelli AO, Yang X, Lintner RE, et al. Mutational processes shape the landscape of TP53 mutations in human cancer. Nat Genet. 2018;50(10):1381–1387. doi:10.1038/s41588-018-0204-y. [30224644] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 32. Monti P, Perfumo C, Bisio A, et al. Dominant-negative features of mutant TP53 in germline carriers have limited impact on cancer outcomes. Mol Cancer Res. 2011;9(3):271–279. doi:10.1158/1541-7786.MCR-10-0496. [21343334] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 33. Shahbandi A, Jackson JG. Analysis across multiple tumor types provides no evidence that mutant p53 exerts dominant negative activity. NPJ Precis Oncol. 2019;3:1. doi:10.1038/s41698-018-0074-x. [30623031] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 34. Frebourg T, Lagercrantz SB, Oliveira C, Magenheim R, Evans DG; European Reference Network GENTURIS. Guidelines for the Li-Fraumeni and heritable TP53-related cancer syndromes. Eur J Hum Genet. 2020;28(10):1379–1386. doi:10.1038/s41431-020-0638-4. [32457520] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 35. Schon K, Tischkowitz M. Clinical implications of germline mutations in breast cancer: TP53. Breast Cancer Res Treat. 2018;167(2):417–423. doi:10.1007/s10549-017-4531-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 36. Kasper E, Angot E, Colasse E, et al. Contribution of genotoxic anticancer treatments to the development of multiple primary tumours in the context of germline TP53 mutations. Eur J Cancer. 2018;101:254–262. doi:10.1016/j.ejca.2018.06.011. [DOI] [PubMed] [Google Scholar]
- 37. Mai PL, Best AF, Peters JA, et al. Risks of first and subsequent cancers among TP53 mutation carriers in the National Cancer Institute Li-Fraumeni syndrome cohort. Cancer. 2016;122(23):3673–3681. doi:10.1002/cncr.30248. [27496084] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 38. Kratz CP, Achatz MI, Brugières L, et al. Cancer screening recommendations for individuals with Li-Fraumeni syndrome. Clin Cancer Res. 2017;23(11):e38–e45. doi:10.1158/1078-0432.CCR-17-0408. [28572266] [DOI] [PubMed] [Google Scholar]
- 39. Villani A, Shore A, Wasserman JD, et al. Biochemical and imaging surveillance in germline TP53 mutation carriers with Li-Fraumeni syndrome: 11 year follow-up of a prospective observational study. Lancet Oncol. 2016;17(9):1295–1305. doi:10.1016/S1470-2045(16)30249-2. [27501770] [DOI] [PubMed] [Google Scholar]
- 40. Tabori U, Shlien A, Baskin B, et al. TP53 alterations determine clinical subgroups and survival of patients with choroid plexus tumors. J Clin Oncol. 2010;28(12):1995–2001. doi:10.1200/J Clin Oncol.2009.26.8169. [DOI] [PubMed] [Google Scholar]
- 41. Wagner J, Portwine C, Rabin K, Leclerc JM, Narod SA, Malkin D. High frequency of germline p53 mutations in childhood adrenocortical cancer. J Natl Cancer Inst. 1994;86(22):1707–1710. [DOI] [PubMed] [Google Scholar]
- 42. Wasserman JD, Novokmet A, Eichler-Jonsson C, et al. Prevalence and functional consequence of TP53 mutations in pediatric adrenocortical carcinoma: a children’s oncology group study. J Clin Oncol. 2015;33(6):602–609. doi:10.1200/JCO.2013.52.6863. [25584008] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 43. Hettmer S, Archer NM, Somers GR, et al. Anaplastic rhabdomyosarcoma in TP53 germline mutation carriers. Cancer. 2014;120(7):1068–1075. doi:10.1002/cncr.28507. [24382691] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 44. Waszak SM, Northcott PA, Buchhalter I, et al. Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. Lancet Oncol. 2018;19(6):785–798. doi:10.1016/S1470-2045(18)30242-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 45. Fortuno C, James PA, Spurdle AB. Current review of TP53 pathogenic germline variants in breast cancer patients outside Li-Fraumeni syndrome. Hum Mutat. 2018;39(12):1764–1773. doi:10.1002/humu.23656. [30240537] [DOI] [PubMed] [Google Scholar]
- 46. Gonzalez KD, Buzin CH, Noltner KA, et al. High frequency of de novo mutations in Li-Fraumeni syndrome. J Med Genet. 2009;46(10):689–693. doi:10.1136/jmg.2008.058958. [19556618] [DOI] [PubMed] [Google Scholar]
- 47. Renaux-Petel M, Charbonnier F, Théry JC, et al. Contribution of de novo and mosaic TP53 mutations to Li-Fraumeni syndrome. J Med Genet. 2018;55(3):173–180. doi:10.1136/jmedgenet-2017-104976. [29070607] [DOI] [PubMed] [Google Scholar]
- 48. Razavi P, Li BT, Brown DN, et al. High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants. Nat Med. 2019;25(12):1928–1937. doi:10.1038/s41591-019-0652-7. [31768066] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 49. Hughley R, Karlic R, Joshi H, Turnbull C, Foulkes WD, Polak P . Etiologic index—a case-only measure of BRCA1/2-associated cancer risk. N Engl J Med. 2020;383(3):286–288. doi:10.1056/NEJMc1913988. [32668122] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 50. Easton DF, Pharoah PDP, Antoniou AC, et al. Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med. 2015;372(23):2243–2257. doi:10.1056/NEJMsr1501341. [26014596] [DOI] [PMC free article] [PubMed] [Google Scholar]
- 51. Dorling L, Carvalho S, Allen J, et al. ; Breast Cancer Association Consortium. Breast cancer risk genes—association analysis in more than 113,000 women. N Engl J Med. 2021;384(5):428–439. doi:10.1056/NEJMoa1913948. [33471991] [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Data Availability Statement
Deidentified molecular data from LFS tumors in the study are available upon request.